Ascaris suum - public RNASeq studies
Table of Contents
- Ascaris suum transcriptome (RNA-Seq) data
- Ascaris suum Genome sequencing and assembly
- Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells
- De novo nematode genome sequencing project to sequence, Ascaris suum, or Pig Roundworm.
- Transcription in Pronuclei and One- to Four-Cell Embryos Drives Early Development in a Nematode
- Comparative Genome Analysis of Programmed DNA Elimination in Nematodes (Ascaris)
- 3 other studies
Analysed
SRP005511: Ascaris suum transcriptome (RNA-Seq) data
Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver
Design: 6 conditions
| Condition | num. replicates | Developmental stage | Organism part | Sex |
|---|---|---|---|---|
| L2 larvae | 1 | L2 | whole organism | mixed |
| embryos | 5 | embryo 0 - 64 hr | whole organism | mixed |
| female reproductive system | 1 | adult | female reproductive system | female |
| ovary | 1 | adult | ovary | female |
| testis | 6 | adult | testis | male |
| whole male | 1 | adult | whole organism | male |
SRP010159: Ascaris suum Genome sequencing and assembly
Beijing Genomics Institute
Ascaris suum draft genome. (Jex .. Gasser, 2011)
Design: 8 conditions
| Condition | num. replicates | Developmental stage | Geographic location | Host | Host tissue | Individual | Sex |
|---|---|---|---|---|---|---|---|
| Adult female individual 1 | 2 | adult | Belgium | Sus scrofa | 1 | female | |
| Adult female individual 2 | 2 | adult | Belgium | Sus scrofa | 2 | female | |
| Adult male individual 3 | 2 | adult | Belgium | Sus scrofa | 3 | male | |
| Adult male individual 4 | 2 | adult | Belgium | Sus scrofa | 4 | male | |
| Pooled L3 stage eggs | 1 | egg | Belgium | Sus scrofa | mixed | ||
| Pooled L3 stage from pig lungs | 1 | L3 | Belgium | Sus scrofa | lungs | mixed | |
| Pooled L3 stage isolated from pig livers | 1 | L3 | Belgium | Sus scrofa | liver | mixed | |
| Pooled L4 stage from pig small intestine | 1 | L4 | Belgium | Sus scrofa | small intestine | mixed |
SRP013573: Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells
Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver
Silencing of germline-expressed genes by DNA elimination in somatic cells. (Wang .. Davis, 2012)
Design: 10 conditions
| Condition | num. replicates | Developmental stage | Organism part | Sample name | Source name | Strain | Timepoint |
|---|---|---|---|---|---|---|---|
| 24hr | 1 | embryo | 24hr | 24hr (1-cell) embryos | North American wild population | 24 hr | |
| 46hr | 1 | embryo | 46hr | 46hr (1-2-cell) embryos | North American wild population | 46 hr | |
| 64hr | 1 | embryo | 64hr | 64hr (2-4-cell) embryos | North American wild population | 64 hr | |
| female carcass | 1 | adult | carcass | female carcass | muscle, hypodermis, pharynx, and neurons | North American wild population | |
| intestine | 1 | adult | intestine | intestine | intestine | North American wild population | |
| larvae | 1 | larvae | larvae | 7 days - Larvae L2 | North American wild population | ||
| male carcass | 1 | adult | carcass | male carcass | muscle, hypodermis, pharynx, and neurons | North American wild population | |
| muscle | 1 | adult | muscle | muscle | muscle (and hypodermis) | North American wild population | |
| ovary | 1 | adult | ovary | ovary | ovary germinal zone | North American wild population | |
| testis | 1 | adult | testis | testis | testis germinal zone | North American wild population |
SRP013609: De novo nematode genome sequencing project to sequence, Ascaris suum, or Pig Roundworm.
The Genome Institute
Design: 15 conditions
| Condition | num. replicates |
|---|---|
| anterior intestine | 7 |
| female intestine | 2 |
| female pharynx | 2 |
| head | 2 |
| male head | 2 |
| male intestine | 2 |
| male pharynx | 2 |
| mid intestine | 4 |
| ovary | 2 |
| posterior intestine | 7 |
| seminal vesicle | 2 |
| testis | 2 |
| uterus | 2 |
| whole intestine | 4 |
| whole worm | 4 |
SRP021466: Transcription in Pronuclei and One- to Four-Cell Embryos Drives Early Development in a Nematode
Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver
Design: 17 conditions
| Condition | num. replicates | Developmental stage | Sample name | Strain | Timepoint |
|---|---|---|---|---|---|
| L1 | 1 | larvae | North American wild population | L1 | |
| L2 | 1 | larvae | L2 | North American wild population | L2 |
| embryo, 1 day | 1 | embryo | North American wild population | 1 day | |
| embryo, 116 hours | 1 | embryo | North American wild population | 116 hours | |
| embryo, 2h hours | 1 | embryo | North American wild population | 2h hours | |
| embryo, 3 days | 1 | embryo | North American wild population | 3 days | |
| embryo, 46 hours | 1 | embryo | North American wild population | 46 hours | |
| embryo, 5 days | 1 | embryo | North American wild population | 5 days | |
| embryo, 64 hours | 3 | embryo | North American wild population | 64 hours | |
| embryo, 7 days | 2 | embryo | North American wild population | 7 days | |
| embryo, 96 hours | 1 | embryo | North American wild population | 96 hours | |
| oocyte - ribozero | 1 | female germline | oocyte - ribozero | North American wild population | |
| oocyte - total | 1 | female germline | oocyte - total | North American wild population | |
| oocyte with wall | 1 | female germline | oocyte with wall | North American wild population | |
| oocyte with wall - ribozero | 1 | female germline | oocyte with wall - ribozero | North American wild population | |
| oocyte with wall - total | 1 | female germline | oocyte with wall - total | North American wild population | |
| zygote | 7 | zygote | North American wild population |
SRP108384: Comparative Genome Analysis of Programmed DNA Elimination in Nematodes (Ascaris)
Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver
Comparative genome analysis of programmed DNA elimination in nematodes. (Wang .. Davis, 2017)
Design: 10 conditions
| Condition | num. replicates | Organism part | Sex | Strain |
|---|---|---|---|---|
| female diplotene | 1 | diplotene | female | North American wildtype |
| female early pachytene | 1 | early pachytene | female | North American wildtype |
| female late pacheytene | 1 | late pacheytene | female | North American wildtype |
| female mitotic region | 1 | mitotic region | female | North American wildtype |
| female oocyte | 1 | oocyte | female | North American wildtype |
| male mitotic region | 1 | mitotic region | male | North American wildtype |
| male post-meiotic region | 1 | post-meiotic region | male | North American wildtype |
| male seminal vesicle | 1 | seminal vesicle | male | North American wildtype |
| male spermatids | 1 | spermatids | male | North American wildtype |
| male spermatogenesis | 1 | spermatogenesis | male | North American wildtype |
Other
These studies are available in ENA, and the reads successfully align to our genomes.
They have not been included in our analysis for one of the following reasons:
Failed to meet minimal criteria for differential expression analysis, failure to pass data quality filters, or we were unable to interpret accompanying metadata.
SRP005510: Ascaris suum Small RNA-Seq data
Richard E. Davis Lab, Biochemistry and Molecular Genetics, University of Colorado Denver
51 runs in ENA
SRP013430: Ascaris suum Chromatin Diminution
University of Colorado School of Medicine
Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. (Wang .. Davis, 2011)
Silencing of germline-expressed genes by DNA elimination in somatic cells. (Wang .. Davis, 2012)
10 runs in ENA
SRP140708: Dual RNA-Seq of Ascaris suum larvae (L3) and Sus scrofa cells (IPEC-J2)
Release 18 - April 2023
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